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Ruth Lydia Schmidt
Microbial Ecologist & Data Scientist
A dynamic and resourceful microbial ecologist with 8 years of experience in microbiome research, data analysis and science communication, with strong leadership and a broad set of technical and interpersonal skills. Passionate about finding sustainable solutions for environmental issues through the combination of research, data and policy.
Education
Ph.D. in Microbial Ecology
Wageningen University & Netherlands Institute of Ecology (NIOO)
Title: Volatile communication between fungi and bacteria
Wageningen, The Netherlands
10/2017
M.S. in Biotechnology
Graz University of Technology
Graz, Austria
12/2012
B.Sc. in Molecular Biology
Graz University of Technology
Graz, Austria
09/2010
Research Experience
Mitacs Postdoctoral Fellow
Institut national de la recherche scientifique (INRS) & Plotly
Montréal, Canada
01/2020 - Present
- Developing open-source visualization apps for omic data in microbiome research using Ploty’s Dash R and Dash Bio libraries.
Visiting JSPS Postdoctoral Fellow
Kochi Core Center
Kochi, Japan
01/2020 - 03/2020
- Developed PCR-based screening method for detection of terpene synthase genes (TPS) across terrestrial and aquatic environments.
- Performed amplicon sequencing of PCR products and bioinformatics data analysis.
Consultant
International Union for Conservation of Nature (IUCN)
remote
07/2019-10/2019
- Contributed to a global report on soil biodiversity in agro-ecosystem health.
Postdoctoral Fellow
Institut national de la recherche scientifique (INRS), Labo Yergeau
Montréal, Canada
02/2018 - 12/2019
- Research on microbial solutions to drought in agriculture.
- Led lab and field studies with wheat under drought conditions.
- Conducted analysis of omic data (quantitative metagenomics, metatranscriptomics, metabolomics).
- Co-supervised 4 PhD students and 2 Master students.
- Presented findings at 6 international conferences.
- Collaborated with researchers in The Netherlands (Netherlands Institute of
Ecology) & UK (Plymouth Marine Laboratory).
PhD Candidate
Netherlands Institute of Ecology & Wageningen University, Garbeva Group
Wageningen, The Netherlands
02/2013 - 10/2018
- Characterized molecular mechanism underlying volatile interaction in soil microbes using a combination of omic, microbiological, and analytical (GC-MS) approaches (link to video about research).
- Analyzed omic data (proteomics, metabolomics) and developed workflow for metabolomic data analysis.
- Mentored 4 undergraduate and 1 graduate student on molecular biology research projects.
- Collaborated with international research institutes and universitites in Germany (Max-Planck Institute for Chemical Ecology, Jena & Center for Functional Genomics of Microbes, Greifswald), US (Institute for Genome Sciences, Baltimore) & Sweden (Swedish University of Agricultural Sciences) on genomics and proteomics projects.
University assistant
Graz University of Technology
Graz, Austria
10/2010-12/2012
- Led and conducted field study on the effect of biocontrol agents in field in Egypt.
- Performed analysis of 16S rRNA sequencing data, and measurement and analysis of analytical data (LC-MS).
Teaching Experience
Instructor in two days hands-on course on proteomics
Netherlands Institute of Ecology
Wageningen, The Netherlands
09/2015
Teaching Assistant in Laboratory Course in Environmental Biotechnology
Graz University of Technology
Graz, Austria
10/2013
Research Assistant in Laboratory Course in Biochemistry and Molecular Biology
Karl-Franzens University
Graz, Austria
06/2012
Grants & awards
Mitacs Postdoctoral Fellowship (60,000 CAD)
Visualization of multi-omics data in microbiome research
Montréal, Canada
2019
Japan Society for the Promotion of Science (JSPS) Award (8,000 CAD)
Uncovering microbial chemical ecology in the extreme sub-seafloor environment
Kochi Core Centre, Japan
2019
Coalesce BioArt residency (2,000 USD)
Microbial Scents and Olfactory Prosthesis for the Future
Coalesce: Center for Biological Art, University at Buffalo, USA
2019
Quebec Centre for Biodiversity Science (QCBS) Travel grant (1,500 CAD)
International Phytobiome meeting
Montpellier, France
2018
QCBS Seed grant (5,000 CAD)
Aural soilscapes: creating ecological consciousness to global warming
Montréal, Canada
2018
QCBS Travel grant (1,500 CAD)
ISME17 meeting
Leipzig, Germany
2018
International Society of Chemical Ecology (ISCE) Travel Grant (1,000 USD)
Annual Meeting ISCE17
Kyoto, Japan
2017
Best Talk Award (150 USD)
Annual Meeting ISCE17
Kyoto, Japan
2017
Federation of European Microbiological Societies (FEMS) Research Grant (5,000 Eur)
Research on fungal genomics at the Swedish University of Agricultural Sciences (SLU)
Uppsala, Sweden
2017
International Society for Microbial Ecology (ISME) Travel Grant (800 Eur)
ISME16 meeting
Montréal, Canada
2016
FEMS Meetings Attendance Grant (300 Eur)
Ecology of Soil Microorganisms meeting
Prague, Czech Republic
2015
Best Poster Award (100 Eur)
Ecology of Soil Microorganisms meting
Prague, Czech Republic
2015
Presentations
Kochi Core Center (talk)
Uncovering microbial terpenes in the extreme sub-seafloor environment.
Kochi, Japan
02/2020
International Society of Chemical Ecology, ISCE 35 (talk)
Microbial chemical ecology: past, present and future.
Atlanta, USA
06/2019
Second International Holobiont meeting (talk)
How microbial volatiles help plants survive in times of drought.
Montréal, Canada
05/2019
Quebec Centre for Biodiversity Science Annual Symposium (talk)
Microbial aromas might help plants survive drought.
Montréal, Canada
12/2018
International Phytobiomes Conference (poster)
Microbial terpenes in the plant holobiont as a strategy to adapt to drought.
Montpellier, France
12/2018
International Symposium on Microbial Ecology, ISME 17 (talk)
Do bacteria and fungi have a fragrant language all their own?
Leipzig, Germany
08/2018
International Symposium on Microbial Ecology, ISME 17 (speaker in roundtable session)
Microbial chemical ecology: intra- and interspecies communication.
Leipzig, Germany
08/2018
Champalimaud Centre for the Unknown
Microworld - the most powerful life on earth.
Lisbon, Portugal
06/2018
International Society of Chemical Ecology, ISCE 34 (talk)
Terpenes as lingua franca between fungi and bacteria.
Kyoto, Japan
08/2017
International Symposium on Microbial Ecology, ISME 16 (poster)
Transcriptional responses of a beneficial soil bacterium to volatiles of a plant pathogen.
Montréal, Canada
08/2016
Ecology of soil microorganisms, ESM (poster)
Microbial small talk: Volatiles in fungal-bacterial interactions.
Prague, Czech Republic
12/2015
4th International student conference on Microbial Communication, MiCom (talk)
Chemical dialogues: The ability of bacteria to sense fungal volatiles.
Jena, Germany
04/2014
CNRS-Jacques Monod conference: bacterial–fungal interactions: a federative field for fundamental and applied microbiology
The role of fungal volatiles as signaling compounds in bacterial-fungal interactions.
Roscoff, France
12/2013
Boston Bacterial Meeting, BBM (poster)
Microbial interactions via secondary metabolites in soil.
Boston, USA
06/2013
Netherlands Annual Ecology Meeting, NERN (poster)
The best bacterial competitive strategies in the rhizosphere.
Lunteren, The Netherlands
02/2013
Publications
A Gaseous Milieu: Extending the Boundaries of the Rhizosphere.
Trends in microbiology. DOI: 10.1016/j.tim.2020.02.016
N/A
2020
de la Porte, A., Schmidt, R., Yergeau, É., & Constant, P.
Microbe-driven chemical ecology: past, present and future.
ISME J. DOI: 10.1038/s41396-019-0469-x
N/A
2019
Schmidt, R., Ulanova, D., Wick, L. Y., Bode, H. B., & Garbeva, P.
Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum.
FEMS Microbiol Ecol. DOI: 10.1093/femsec/fiy078
N/A
2018
Schmidt, R., Durling, M. B., de Jager, V., Menezes, R. C., Nordkvist, E., Svatoš, A., Dubey, M., Lauterbach, L., Dickschat, J. S., Karlsson, M., & Garbeva, P.
Fifty Percent Human - how art brings us in touch with our microbial cohabitants.
Microb Biotechnol.DOI: 10.1111/1751-7915.13285
N/A
2018
Bäumel, S., Tytgat, H., Nemec, B., Schmidt, R., Chia, L. W., & Smidt, H.
The future of ecology is collaborative, inclusive and deconstructs biases.
Nat Ecol Evol. DOI: 10.1038/s41559-017-0445-7
N/A
2018
Ramirez, K. S., Berhe, A. A., Burt, J., Gil-Romera, G., Johnson, R. F., Koltz, A. M., Lacher, I., McGlynn, T., Nielsen, K. J., Schmidt, R., Simonis, J. L., terHorst, C. P., & Tuff, K.
Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C.
Sci Rep. DOI: 10.1038/s41598-017-00893-3
N/A
2017
Schmidt, R., Jager, V., Zühlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., Ijcken, W. V., Sleutels, F., Boer, W., Riedel, K., & Garbeva, P.
Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut.
Front Microbiol. DOI: 10.3389/fmicb.2016.01079
N/A
2016
Adam, E., Groenenboom, A. E., Kurm, V., Rajewska, M., Schmidt, R., Tyc, O., Weidner, S., Berg, G., de Boer, W., & Falcão Salles, J.
Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions.
Front Microbiol. DOI: 10.3389/fmicb.2015.01495
N/A
2016
Schmidt, R., Etalo, D. W., de Jager, V., Gerards, S., Zweers, H., de Boer, W., & Garbeva, P.
Volatile affairs in microbial interactions.
ISME J. DOI: 10.1038/ismej.2015.42
N/A
2016
Schmidt, R., Cordovez, V., de Boer, W., Raaijmakers, J., & Garbeva, P.
Exploring the genomic traits of fungus-feeding bacterial genus Collimonas.
BMC Genomics. DOI: 10.1186/s12864-015-2289-3
N/A
2015
Song, C., Schmidt, R., de Jager, V., Krzyzanowska, D., Jongedijk, E., Cankar, K., Beekwilder, J., van Veen, A., de Boer, W., van Veen, J. A., & Garbeva, P.
Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants.
Front Microbiol. DOI: 10.3389/fmicb.2013.00400
N/A
2014
Schmidt, R., Köberl, M., Mostafa, A., Ramadan, E. M., Monschein, M., Jensen, K. B., Bauer, R., & Berg, G.
The microbiome of medicinal plants: diversity and importance for plant growth, quality and health.
Front Microbiol. DOI: 10.3389/fmicb.2014.00064
N/A
2013
Köberl, M., Schmidt, R., Ramadan, E. M., Bauer, R., & Berg, G.
Manuscripts in preparation
Soil hydrogen enrichment increases H2-oxiding bacterial activity and changes microbial community structure and function (under review).
Soil Biol. Biochem.
N/A
N/A
Wang X., Schmidt R., Constant P., & Yergeau E.
Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions (submitted).
Appl. Environ. Microbiol.
N/A
N/A
Schmidt R., Wang X., Garbeva, P., & Yergeau E.
Infochemicals in terrestrial plants and marine macroalgal holobionts under a changing climate (under review).
New Phytologist.
N/A
N/A
Schmidt R., & Saha, M.